Computational Investigation Identified Potential Chemical Scaffolds for Heparanase as Anticancer Therapeutics

Heparanase (Hpse) is an endo-β-D-glucuronidase capable of cleaving heparan sulfate side chains. Its upregulated expression is implicated in tumor growth, metastasis and angiogenesis, thus making it an attractive target in cancer therapeutics. Currently, a few small molecule inhibitors have been reported to inhibit Hpse, with promising oral administration and pharmacokinetic (PK) properties. In the present study, a ligand-based pharmacophore model was generated from a dataset of well-known active small molecule Hpse inhibitors which were observed to display favorable PK properties. The compounds from the InterBioScreen database of natural (69,034) and synthetic (195,469) molecules were first filtered for their drug-likeness and the pharmacophore model was used to screen the drug-like database. The compounds acquired from screening were subjected to molecular docking with Heparanase, where two molecules used in pharmacophore generation were used as reference. From the docking analysis, 33 compounds displayed higher docking scores than the reference and favorable interactions with the catalytic residues. Complex interactions were further evaluated by molecular dynamics simulations to assess their stability over a period of 50 ns. Furthermore, the binding free energies of the 33 compounds revealed 2 natural and 2 synthetic compounds, with better binding affinities than reference molecules, and were, therefore, deemed as hits. The hit compounds presented from this in silico investigation could act as potent Heparanase inhibitors and further serve as lead scaffolds to develop compounds targeting Heparanase upregulation in cancer.     

微纳层叠聚丙烯腈凝胶流动特性的数值模拟研究

建立了层叠流道的三维模型和有限元网格模型，根据流变测试数据，采用Polymat对物料的黏度模型参数进行拟合，并利用Polyflow软件对聚丙烯腈（PAN）凝胶在层叠流道内的三维等温流动过程进行了数值模拟分析。研究发现，当入口流量增大时，层叠流道出口速度的不均匀性增加；沿流动方向流道内压力逐渐降低，并在出口处降低至同一最低值；流道进出口压力差与入口流量大小具有正相关性；在流道的中心截面上剪切速率分布均匀，波动较小。     

Thermal desorption and pyrolysis direct analysis in real time mass spectrometry of Nafion membrane

Perfluorosulfonic acid ionomer membranes have been widely used as proton conducting membranes in various electrochemical processes such as polymer electrolyte fuel cells and water electrolysis. While their thermal stability has been studied by thermogravimetry and analysis of low molecular weight products, their decomposition mechanism is little understood. In this study a newly developed methodology of thermal desorption and pyrolysis in combination with direct analysis in real time mass spectrometry is applied for Nafion membrane. An ambient ionization source and a high-resolution time-of-flight mass spectrometer enabled unambiguous assignment of gaseous products. Thermal decomposition is initiated by side chain detachment above 350°C, which leaves carbonyls on the main chain at the locations of the side chains. Perfluoroalkanes are released above 400°C by main chain scission and their further decomposition products dominate above 500 °C. DFT calculation of reaction energies and barrier heights of model compounds support proposed decomposition reactions.     

An integrated dimensionality reduction and surrogate optimization approach for plant-wide chemical process operation

With liquefied natural gas becoming increasingly prevalent as a flexible source of energy, the design and optimization of industrial refrigeration cycles becomes even more important. In this article, we propose an integrated surrogate modeling and optimization framework to model and optimize the complex CryoMan Cascade refrigeration cycle. Dimensionality reduction techniques are used to reduce the large number of process decision variables which are subsequently supplied to an array of Gaussian processes, modeling both the process objective as well as feasibility constraints. Through iterative resampling of the rigorous model, this data-driven surrogate is continually refined and subsequently optimized. This approach was not only able to improve on the results of directly optimizing the process flow sheet but also located the set of optimal operating conditions in only 2 h as opposed to the original 3 weeks, facilitating its use in the operational optimization and enhanced process design of large-scale industrial chemical systems.     

In Silico Investigation of Potential Applications of Gamma Carbonic Anhydrases as Catalysts of CO2 Biomineralization Processes: A Visit to the Thermophilic Bacteria Persephonella hydrogeniphila,Persephonella marina,Thermosulfidibacter takaii,and Thermus thermophilus

Carbonic anhydrases (CAs) have been identified as ideal catalysts for CO₂ sequestration. Here, we report the sequence and structural analyses as well as the molecular dynamics (MD) simulations of four γ-CAs from thermophilic bacteria. Three of these, Persephonella marina, Persephonella hydrogeniphila, and Thermosulfidibacter takaii originate from hydrothermal vents and one, Thermus thermophilus HB8, from hot springs. Protein sequences were retrieved and aligned with previously characterized γ-CAs, revealing differences in the catalytic pocket residues. Further analysis of the structures following homology modeling revealed a hydrophobic patch in the catalytic pocket, presumed important for CO₂ binding. Monitoring of proton shuttling residue His69 (P. marina γ-CA numbering) during MD simulations of P. hydrogeniphila and P. marina’s γ-CAs (γ-PhCA and γ-PmCA), showed a different behavior to that observed in the γ-CA of Escherichia coli, which periodically coordinates Zn²⁺. This work also involved the search for hotspot residues that contribute to interface stability. Some of these residues were further identified as key in protein communication via betweenness centrality metric of dynamic residue network analysis. T. takaii’s γ-CA showed marginally lower thermostability compared to the other three γ-CA proteins with an increase in conformations visited at high temperatures being observed. Hydrogen bond analysis revealed important interactions, some unique and others common in all γ-CAs, which contribute to interface formation and thermostability. The seemingly thermostable γ-CA from T. thermophilus strangely showed increased unsynchronized residue motions at 423 K. γ-PhCA and γ-PmCA were, however, preliminarily considered suitable as prospective thermostable CO₂ sequestration agents.     

爆破位置对深凹露天矿山炮烟扩散的影响研究

深凹露天矿山由于其特殊的结构,爆破产生的炮烟扩散稀释较为困难,严重危害生产作业人员的生命安全与健康。基于实际矿山构建了深凹露天矿山的二维物理及数学模型,采用非稳态数值分析方法研究了不同爆破位置下,深凹露天矿山采坑内爆破炮烟的扩散规律。研究结果表明：不同爆破位置下,露天采坑内均出现复环流,爆破点位置是影响露天采坑内风流结构特征的重要因素；露天采坑内的炮烟最高浓度均随着时间变化而逐渐下降,但下降的速率逐步减小,呈现三个阶段的下降趋势；爆破位置位于背风侧时露天采坑内的炮烟最高浓度和降至安全浓度所需时间远高于迎风侧三个爆破位置；随着背风侧爆破点距采坑底部距离的减小,炮烟最高浓度及降至安全浓度所需时间先降低后增加,炮烟最高浓度及降至安全浓度所需时间随着迎风侧爆破位置距采坑底部距离的减小而增加。研究结果对于指导深凹露天矿山企业合理组织爆破后的生产作业和保障作业人员安全具有重要意义。     

地应力条件下的凿岩爆破数值模拟

为了研究地应力对凿岩爆破的影响,采用DDA方法模拟爆炸应力波作用下考虑地应力条件时的单孔和多孔凿岩爆破破岩过程。模拟发现,随着初始地应力水平的增加,裂纹扩展半径和破岩区域面积减小,裂纹发育主方向趋于地应力的最大主应力方向,初始地应力对裂纹的抑制和引导作用明显;初始地应力水平的增加,对拉伸裂纹的抑制作用更为显著,从而降低了拉伸破坏对爆破破岩的贡献。模拟也表明,在初始地应力存在的条件下,通过对爆破载荷和炮孔布置进行针对性的优化,可以克服地应力带来的影响,并取得预期的爆破效果。本研究对地应力条件下的凿岩爆破工程具有理论和参考意义。     

Optimization of PEMFC system operating conditions based on neural network and PSO to achieve the best system performance

PEMFC system is a complex new clean power system. Based on MATLAB/Simulink, this paper develops a system-level dynamic model of PEMFC, including the gas supply system, hydrogen supply system, hydrothermal management system, and electric stack. The neural network fits the electric stack model to the simulation data. The effects of different operating conditions on the PEMFC stack power and system efficiency are analyzed. Combining the power of the reactor and the system efficiency to define the integrated performance index, the particle swarm optimization (PSO) algorithm is introduced to optimize the power density and system efficiency of the PEMFC with multiple objectives. The final optimal operating point increases the power density and system efficiency by 1.33% and 12.8%, respectively, which maximizes the output performance and reduces the parasitic power.     

内含实体对H型垂直轴风力机气动性能的影响

以H型垂直轴风力机及其内含圆柱形实体为研究对象,对NACA0018翼型的五叶片H型垂直轴风力机的气动性能进行数值模拟和实验验证。分析8种不同直径的内含圆柱体,在内含实体截面积占风轮迎风面积之比分别为21.2%、50.0%和76.9%时,风力机风能利用率的峰值分别下降8.04%、20.7%及74.3%。结果表明：随着内含实体直径的增大,风能利用率的峰值逐渐减小,开始较为缓慢,达到一定值时快速下降。小直径内含实体主要影响叶片在下风区的转矩,对风能利用率的影响较小,而大直径内含实体还会影响叶片在上风区的转矩,其风能利用率迅速减小。对于内含固定直径的实体,比如在现有建筑物外侧安装风力机时,其风轮半径的选择需综合考虑风能利用率和风力机的建造成本两方面的因素。研究结果可为建筑物与垂直轴风力机进行有效结合以提高风能的利用提供参考。     

Combining a new baseboard radiator with a fan coil system for improving heating performance and reduce energy consumption

In the present work, the heating performance of a new system combined with a new modified baseboard radiator and fan coil is investigated. Using longitudinal fins with special geometry and also forced airflow at the end of the system causes that at the lower inlet water temperature compared with the conventional models, higher heat output rate be obtained. The heat output rate of the new modified system is obtained by experimental metrology based on the European Standard No. EN-442. Temperature and velocity distribution in the room space is done by simulation of the modified system in the Flovent software. Computational fluid dynamics (CFD) results are validated against experimental results and there is a good agreement between them. Also, the energy consumption of the system during the winter season is calculated in TRANSYS software. Experimental results show that the heat output rate of a new modified heating system with inlet water temperature in the range of 45–55°C is on average 4.17 times higher compared with the conventional model. CFD simulation also showed that the combined system provides good thermal comfort conditions. Energy consumption of the new system reduced about 13% compared with conventional models.